| getLogLikelihoodGivenRelation {GenABEL} | R Documentation |
Compute logLik of genotypes of person 1 given genotypes of person 2 and assumed relation between the two persons (expressed with transition probability matrix; as returned with 'makeTransitionMatrix').
getLogLikelihoodGivenRelation(bGenotype1, bGenotype2,
TransitionMatrix, q)
bGenotype1 |
blurred genotype of person 1 |
bGenotype2 |
blurred genotype of person 2 |
TransitionMatrix |
transition probability matrix |
q |
vector of effect allele frequencies |
Yurii Aulchenko
require(GenABEL.data) data(srdta) # select 10 first SNPs df <- srdta[,1:10] # compute effect allele freq EAF <- summary(gtdata(df))$"Q.2" # get genotypes of first 2 people g1 <- as.numeric(df[1:2,]) # blur all genotypes of person 1; use HWE to infer missing bg1 <- blurGenotype(g1[1,],q=EAF) # blur all genotypes of person 2; use HWE to infer missing bg2 <- blurGenotype(g1[2,],q=EAF) # generate sib-sib transision matrices trss <- makeTransitionMatrix(EAF,nmei=c(2,2)) getLogLikelihoodGivenRelation(bg1,bg2,trss,EAF)